Vertical microbime transmission

We are honored to be recipient of the ERC Starting grant 2016 and we are looking for motivated computational scientists, PhD students, and postdoctoral fellows to join the lab. Take a look at the call and contact me if interested!

Meta'omics for hacking the human microbiome

Our body harbours ~100 trillion microbes which outnumber our own cells.
This microbial diversity (the "microbiome") and its functions are still largely uncharachterized
but we can now try to mine it using cultivation-free sequencing-based metagenomic tools.

We employ experimental meta'omic tools and novel computational approaches to study the diversity of the microbiome and its role in human dysbiosis and infections. Our projects bring together computer scientists,
microbiologists, statisticians, and clinicians.

Main research directions

Next generation computational metagenomic tools.
The potential of metagenomics is only partially expressed due to computational challenges.
We are working on novel methods to profile microbiomes at increased resolution (e.g. strains) and perform large-scale comparative genomics on uncharacterized microbes.

Integrative and machine learning meta'omic approaches.
We develop new machine learning tools to cope with the variability and dimensionality of microbiome profiles
and provide clinically relevant signatures by
integrating complementary meta'omic approaches (e.g. metatrasncriptomics or metaproteomics).

Microbiome-pathogen interaction in human infections.
The role of the microbiome in the acquisition and
development of infections is largely unknown. By coupling longitudinal pathogen/microbiome sequencing we aim understand how the microbiome
can modulate the virulence profile and antibiotic resistance of human infections.

Vertical microbiome transmission.
We study how microbes can be transmitted between different environments with specific focus on how members of the microbiome are vertically
transmitted from mothers to infants at birth and during the first years of age.
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